Biochemistry and Metabolic Pathways Flashcards

Vocabulary flashcards covering enzyme regulation, membrane transport, bioenergetics, carbohydrate metabolism, signaling cascades, and protein/amino acid metabolism.

Free Energy of Activation

The energy difference between the reactants and the transition state that separates reactants and products, determining the overall rate of a chemical reaction.

Active Site

A complex molecular machine on an enzyme that acts as a flexible template to bind substrate, stabilize the transition state, and facilitate product formation.

Michaelis Constant ($K_m$)

The unique substrate concentration at which reaction velocity reaches $\frac{1}{2} V_{\max}$, inversely reflecting an enzyme's affinity for its substrate.

Lineweaver-Burk Plot

A double-reciprocal plot ($\frac{1}{v_0}$ vs. $\frac{1}{[S]}$) that transforms the Michaelis-Menten equation into a straight line with an $x$-intercept of $-\frac{1}{K_m}$ and a $y$-intercept of $\frac{1}{V_{\max}}$.

Competitive Inhibitor

A substance structurally similar to the substrate that binds reversibly to the active site, increasing apparent $K_m$ without affecting $V_{\max}$.

Noncompetitive Inhibitor

An inhibitor that binds to a site other than the active site on either free enzyme or the $ES$ complex, decreasing $V_{\max}$ without changing $K_m$.

Uncompetitive Inhibitor

An inhibitor that binds exclusively to the enzyme-substrate ($ES$) complex, altering both $V_{\max}$ and $K_m$, which cannot be overcome by adding substrate.

Allosteric Enzymes

Multi-subunit enzymes regulated by effectors binding at non-active sites, yielding a sigmoidal velocity curve when plotted against substrate concentration.

Homotropic Effector

An allosteric effector where the substrate itself binds to an allosteric site and enhances catalytic properties at active sites via cooperativity.

Heterotropic Effector

An allosteric effector that is a molecule different from the substrate, often acting in feedback inhibition mechanisms.

Osmosis

The passage of water across a semi-permeable membrane from an area of higher water concentration to lower water concentration to equalize osmotic pressure.

Aquaporins

Specialized membrane channel proteins that facilitate the rapid passage of water molecules across cellular membranes.

Primary Active Transport

A transport process in which energy derived directly from $\text{ATP}$ hydrolysis pumps molecules across biological membranes against their electrochemical gradient.

$$\text{Na}^+\text{-K}^+ \text{ ATPase}$$

A primary active transporter that hydrolyzes $\text{ATP}$ to pump $3\,\text{Na}^+$ ions out of the cell and $2\,\text{K}^+$ ions into the cell per cycle.

Secondary Active Transport

Transport powered indirectly by $\text{ATP}$ hydrolysis, utilizing electrochemical ion gradients established by primary active transport to move solutes against their gradient.

Symporter

A co-transporter that moves two different substrates across a biological membrane in the same direction—one with its concentration gradient and one against it.

Antiporter

A co-transporter that transports two substrates across a biological membrane in opposite directions.

GLUT 2

An insulin-insensitive glucose uniporter located in the liver, kidneys, and pancreas with a high $K_m$ ($15\text{--}20\,\text{mM}$) for removing excess blood glucose.

GLUT 4

An insulin-sensitive glucose transporter present in skeletal muscle and adipose tissue that relocates from intracellular vesicles to the plasma membrane upon insulin stimulation.

SGLT (Sodium-Glucose Symporter)

An active transporter on the apical membrane of intestinal epithelial cells that cotransports sodium and glucose into the cell against the glucose concentration gradient.

Bioenergetics

The transfer and utilization of energy in biologic systems concerning the initial and final energy states of reaction components.

Exergonic Reaction

A favorable, spontaneous chemical reaction that releases energy and exhibits a negative change in free energy ($\Delta G < 0$).

Endergonic Reaction

An unfavorable chemical reaction that requires an input of energy to proceed, exhibiting a positive change in free energy ($\Delta G > 0$).

Gibbs Free Energy Change Equation

The thermodynamic equation $\Delta G = \Delta H - T\Delta S$, where $\Delta H$ represents enthalpy change, $T$ is temperature, and $\Delta S$ is entropy change.

Catabolism

Exergonic metabolic pathways that break down complex nutrients into energy-poor products ($\text{CO}_2$, $\text{H}_2\text{O}$, $\text{NH}_3$) while capturing chemical energy as $\text{ATP}$ and $\text{NADH}$.

Anabolism

Endergonic metabolic pathways that synthesize complex cellular macromolecules from simple precursors, requiring energy input from $\text{ATP}$ and reducing power from $\text{NADPH}$.

Glycolysis

A cytosolic pathway of 10 reactions present in all tissues that breaks down one 6-carbon glucose molecule into two 3-carbon pyruvates, yielding a net of $2\,\text{ATP}$ and $2\,\text{NADH}$.

Hexokinase

A high-affinity (low $K_m$), low-capacity (low $V_{\max}$) enzyme in most tissues that phosphorylates glucose to glucose 6-phosphate at low glucose concentrations.

Glucokinase

A low-affinity (high $K_m$), high-capacity (high $V_{\max}$) isoenzyme IV found in the liver and pancreatic $\beta$-cells that operates primarily following high glucose intake.

Phosphofructokinase-1 (PFK-1)

The key rate-limiting enzyme of glycolysis that converts fructose 6-phosphate to fructose 1,6-bisphosphate, potently activated by fructose 2,6-bisphosphate and $\text{AMP}$.

Cori Cycle

A metabolic pathway where lactate generated by anaerobic glycolysis in peripheral tissues (RBCs, exercising muscle) is transported to the liver and converted back to glucose via gluconeogenesis.

Gluconeogenesis

An anabolic pathway occurring primarily in the liver cytosol during prolonged fasting that synthesizes glucose from non-carbohydrate precursors at the cost of 6 high-energy phosphate bonds per glucose.

Pyruvate Dehydrogenase (PDH) Complex

A mitochondrial matrix complex containing three enzymes ($E_1$, $E_2$, $E_3$) that oxidatively decarboxylates pyruvate to acetyl $\text{CoA}$, producing $\text{CO}_2$ and $\text{NADH}$.

Electron Transport Chain (ETC)

A system of four inner mitochondrial membrane complexes and two mobile carriers that transfer electrons from $\text{NADH}$ and $\text{FADH}_2$ to $\text{O}_2$, pumping protons into the intermembrane space.

ATP Synthase

An inner mitochondrial membrane enzyme composed of a proton-channeling $F_0$ domain and a catalytic $F_1$ domain that harnesses the proton-motive force to synthesize $\text{ATP}$.

Thermogenin (UCP1)

An uncoupling protein in brown adipocyte mitochondria that dissipates the proton gradient without generating $\text{ATP}$, releasing the energy as heat.

Heterotrimeric G-Proteins

Transmembrane-receptor-linked signaling complexes composed of $\alpha$, $\beta$, and $\gamma$ subunits that bind $\text{GDP}$ when inactive and $\text{GTP}$ when activated.

Second Messengers

Intracellular signaling molecules (such as $\text{cAMP}$, $\text{IP}_3$, $\text{DAG}$, and $\text{Ca}^{2+}$) that relay and amplify signals from cell-surface receptors.

Ras

A monomeric GTP-binding small G-protein that switches between $\text{GDP}$ and $\text{GTP}$ bound states to regulate the MAP kinase cascade controlling cell proliferation.

STATs

Signal Transducers and Activators of Transcription; latent cytoplasmic proteins containing $\text{SH-2}$ domains that dock at phosphotyrosines, become phosphorylated, dimerize, and regulate gene transcription in the nucleus.

Nuclear-Initiated Steroid Signaling (NISS)

Classical steroid signaling where lipophilic hormones diffuse across the plasma membrane to bind intracellular receptors that serve as ligand-activated transcription factors.

Membrane-Initiated Steroid Signaling (MISS)

Rapid steroid hormone signaling mediated by receptors located in plasma membrane caveolae that activate intracellular kinase cascades without requiring new protein synthesis.

Glycogen Synthase

The key regulatory enzyme of glycogenesis that uses $\text{UDP-glucose}$ to elongate glycogen chains by forming $\alpha(1\rightarrow 4)$ glycosidic bonds.

Branching Enzyme

Amylo-$\alpha(1\rightarrow 4)\rightarrow \alpha(1\rightarrow 6)$-transglycosylase ($4:6$ transferase); an enzyme that transfers a chain of $6\text{--}8$ glucosyl residues to form an $\alpha(1\rightarrow 6)$ branch point in glycogen.

Glycogen Phosphorylase

The rate-limiting enzyme of glycogenolysis that uses pyridoxal phosphate ($\text{PLP}$) to cleave $\alpha(1\rightarrow 4)$ bonds, releasing glucose 1-phosphate.

Debranching Enzyme

A dual-function enzyme possessing glucanotransferase activity (moving 3 glucosyl units) and amylo-$\alpha(1\rightarrow 6)$ glucosidase activity (releasing free glucose at branch points).

Nitrogen Balance

The physiological state determined by comparing nitrogen intake and protein breakdown ($\text{Nitrogen Balance} = \text{Entries} - \text{Exits}$ in the amino acid pool).

Transamination

The reversible transfer of an amino group from an amino acid to an $\alpha$-ketoacid, catalyzed by aminotransferases requiring pyridoxal phosphate (Vitamin $\text{B}_6$).

Alanine Aminotransferase (ALT)

A liver-specific enzyme that catalyzes transamination between alanine and $\alpha$-ketoglutarate, serving as a specific serum biomarker for liver cell damage.

Carbamoyl Phosphate Synthetase I (CPS I)

The mitochondrial, rate-limiting enzyme of the urea cycle that condenses free $\text{NH}_3$ and $\text{CO}_2$ using $2\,\text{ATP}$, strictly requiring $N$-acetylglutamate ($\text{NAG}$) as an allosteric activator.

Hyperammonemia

A toxic elevation of blood ammonia levels ($> 35\,\mu\text{mol/L}$) causing severe central nervous system impairment, stemming from liver failure or inherited urea cycle enzyme deficiencies.

Phenylketonuria (PKU)

An autosomal recessive error of metabolism caused by phenylalanine hydroxylase deficiency, resulting in toxic buildup of phenylalanine and phenyllactate.

Maple Syrup Urine Disease (MSUD)

An autosomal recessive deficiency of the branched-chain $\alpha$-ketoacid dehydrogenase complex ($\text{BCKD}$), leading to toxic accumulation of leucine, isoleucine, and valine.